We have made advances in understanding how heparan sulfate influences FGFR2b signaling on specific progenitor cell types in the epithelium. A major controversy remains in the HS field as to whether HS function requires specific patterns of sulfation or simply charge density. Our data support the hypothesis that patterns of sulfation influence specific HS functions. We propose that distinct patterns of 3-O-sulfation may increase FGFR2b signaling. Hs-3-O-sulfotransferase (Hs3st) enzymes are the largest family of sulfotransferases with seven isoforms;they act at the final stage of the HS biosynthetic pathway, but form the most rare HS modifications. We analyzed the expression of sulfotransferase enzymes in the SMG. The reported function of 3-O-sulfated HS is to bind to antithrombin and the herpes simplex virus glycoprotein, gD1. We demonstrated that Hs3st-modified HS was present on the SMG epithelium and binds to FGFR2b, and that RNAi knockdown of Hs3st reduces morphogenesis and proliferation. We propose that 3-O-sulfated HS in the epithelium binds FGFR2b and increases signaling, end bud proliferation, differentiation, and branching morphogenesis. We are investigating how FGFR2b signaling controls HS production on the cell surface of epithelial end bud progenitor cells. The Kit receptor is a marker of stem/progenitor cells in the SMG and its ligand is stem cell factor (SCF). FGFR2b signaling upregulates Kit expression, which may maintain the end bud progenitor cells. We have also made advances understanding how miRNAs regulate genes involved in epithelial proliferation. The regulation of epithelial proliferation during organ morphogenesis is critical for normal development, as dysregulation is associated with tumor formation. Non-coding miRNAs are post-transcriptional regulators of gene expression that influence key developmental processes such as proliferation and differentiation. We screened miRNA expression in discrete regions of SMGs and identified 267 miRNAs: 85 in the mesenchyme, 36 in the epithelium, and 146 that were present in both tissues. We focused our studies on miR-200c, which accumulates in the epithelial end buds and is reported to be a regulator of genes involved in cancer. Using both loss- and gain-of-function, we demonstrated that miR-200c reduces epithelial proliferation during SMG morphogenesis. To identify the mechanism, we predicted miR-200c target genes and confirmed their expression during SMG development. We demonstrated that miR-200c influences FGFR-mediated epithelial proliferation during branching morphogenesis. Our studies show that miR-200c may be a novel target for controlling epithelial morphogenesis during glandular repair or regeneration. We also investigated the function of the Barx2 transcription factor and FGF10 on ECM remodeling during branching morphogenesis in studies comparing salivary and lacrimal gland development. Our findings highlight differences between the developmental mechanisms of salivary and lacrimal glands branching morphogenesis.